setMaxGapSize

getMaxGapSize

the Max gap size parameter G . default is 30, which was
described to obtained empirically in the CE paper.
the larger the max gap size, the longer the compute time,
but in same cases drastically improved results. Set to -1 for unlimited gap size.

getSeqWeight

Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
By default this is set to 0, meaning no contribution of the sequence alignment score.

Returns:

seqWeight the weight factor (default 0)

setSeqWeight

Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
By default this is set to 0, meaning no contribution of the sequence alignment score.

isOptimizeAlignment

Whether the CE algorithm should extend the best found trace with dynamic programming,
while keeping RMSD at about the same level. This is useful for edge cases with remote homology,
but can be slow for large structures.

Returns:

optimizeAlignment

setOptimizeAlignment

Whether the CE algorithm should extend the best found trace with dynamic programming,
while keeping RMSD at about the same level. This is useful for edge cases with remote homology,
but can be slow for large structures.